Crystallization and preliminary X-ray analysis of bucain, a novel toxin from the Malayan krait Bungarus candidus

Bucain is a three-finger toxin, structurally homologous to snake-venom muscarinic toxins, from the venom of the Malayan krait Bungarus candidus. These proteins have molecular masses of approximately 6000-8000 da and encompass the potent curaremimetic neurotoxins which confer lethality to Elapidae and Hydrophidae venoms. Bucain was crystallized in two crystal forms by the hanging-drop vapour-diffusion technique in 0.1 M sodium citrate pH 5.6, 15% PEG 4000 and 0.15 M ammonium acetate. Form I crystals belong to the monoclinic system space group C2, with unit-cell parameters a = 93.73, b = 49.02, c = 74.09 Angstrom, beta = 111.32degrees, and diffract to a nominal resolution of 1.61 Angstrom. Form II crystals also belong to the space group C2, with unit-cell parameters a = 165.04, b = 49.44, c = 127.60 Angstrom, beta = 125.55degrees, and diffract to a nominal resolution of 2.78 Angstrom. The self-rotation function indicates the presence of four and eight molecules in the crystallographic asymmetric unit of the form I and form II crystals, respectively. Attempts to solve these structures by molecular-replacement methods have not been successful and a heavy-atom derivative search has been initiated.

The X-ray crystallographic structure of Escherichia coli branching enzyme

Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-Angstrom crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH2-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled or branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.

Thermal and Structural Behavior of Dioctadecyldimethylammonium Bromide Dispersions Studied by Differential Scanning Calorimetry and X-Ray Scattering

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Purification, crystallization and preliminary X-ray diffraction analysis of a class P-III metalloproteinase (BmMP-III) from the venom of Bothrops moojeni

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A thermoporometry and small-angle x-ray scattering study of wet silica sonogels as the pore volume fraction is varied

Silica sonogels with different porosities were prepared by acid sono-hydrolysis of tetraethoxysilane. Wet sonogels were studied using small-angle x-ray scattering (SAXS) and differential scanning calorimetry (DSC). The DSC shows a broad thermal peak below the normal water melting point associated with the melting of confined ice nanocrystals, or nanoporosity. The nanopore size distribution was determined from the Gibbs-Thomson equation. As the porosity is increased, a second sharp DSC thermal peak with onset temperature at the water melting point is apparent, which was associated with the melting of ice macrocrystals, or macroporosity. The DSC result could be causing misinterpretation of the macroporosity because water may not be exactly confined in very feeble silica network regions in sonogels with high porosity. The structure of the wet gels can be described fairly well as mutually self-similar mass fractal structures with characteristic length. increasing from similar to 1.8 to similar to 5.4 nm and mass fractal dimension D diminishing discretely from similar to 2.6 to similar to 2.3 as the porosity increases in the range studied. More specifically, such a structure could be described using a two-parameter correlation function gamma(r) similar to r(D-3) exp(-r/xi), which is limited at larger scale by the cut-off distance xi but without a well-defined small scale cut-off distance, at least up to the maximum angular domain probed using SAXS in the present study.

Small-angle X-ray scattering from wet gels prepared from co-hydrolysis of tetraethoxysilane and vinyltriethoxysilane

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Voltage-composition profile and synchrotron X-ray structural analysis of low and high temperature LixCoO2 host material

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mass fractal characteristics of silica sonogels as determined by small-angle x-ray scattering and nitrogen adsorption

A sample series of silica sonogels was prepared using different water-tetraethoxysilane molar ratio (r(w)) in the gelation step of the process in order to obtain aerogels with different bulk densities after the supercritical drying. The samples were analyzed by means of small-angle x-ray-scattering (SAXS) and nitrogen-adsorption techniques. Wet sonogels exhibit mass fractal structure with fractal dimension D increasing from similar to2.1 to similar to2.4 and mass-fractal correlation length xi diminishing from similar to13 nm to similar to2 nm, as r(w) is changed in the nominal range from 66 to 6. The process of obtaining aerogels from sonogels and heat treatment at 500degreesC, in general, increases the mass-fractal dimension D, diminishes the characteristic length xi of the fractal structure, and shortens the fractal range at the micropore side for the formation of a secondary structured particle, apparently evolved from the original wet structure at a high resolution level. The overall mass-fractal dimension D of aerogels was evaluated as similar to2.4 and similar to2.5, as determined from SAXS and from pore-size distribution by nitrogen adsorption, respectively. The fine structure of the secondary particle developed in the obtaining of aerogels could be described as a surface-mass fractal, with the correlated surface and mass-fractal dimensions decreasing from similar to2.4 to similar to2.0 and from similar to2.7 to similar to2.5, respectively, as the aerogel bulk density increases from 0.25 (r(w)=66) up to 0.91 g/cm(3) (r(w)=6).

A study on X-ray irradiation of composite polyaniline LB films

Composite Langmuir-Blodgett (LB) films from polyaniline and cadmium stearate have been irradiated with ionizing X-rays for various exposure times. In the initial stages of X-ray irradiation the absorption peak at 580 nm of an as-deposited film was seen to decrease with a concomitant increase in the absorption in the long wavelength region (700-1100 nm). Upon prolonging the irradiation, the absorption maximum shifted to 800 nm with the LB film color changing to green, characteristic of acid doped polyaniline. The changes in the Fourier transform infrared (FTIR) spectra upon irradiation are also similar to those observed upon acid doping of polyaniline. When compared with acid doping, two major differences were observed for the LB films exposed to X-rays. First, the packing order of the cadmium stearate domains in the composite LB films - as observed by X-ray diffraction - is not affected by the X-ray irradiation. In addition, no significant increase in the DC conductivity was noted after the X-ray exposure whereas similar LB films have their conductivity increased by an order of magnitude upon acid doping. These differences may be explained by considering that the inter-domain contribution to the conductivity is increased by the acid doping because the insulating cadmium stearate domains are destroyed, which does not occur with the X-ray irradiation. (C) 1998 Elsevier B.V. S.A. All rights reserved.

Synthesis, spectroscopic characterization and X-ray crystallographic studies of trans-[PtCl2(PEt3)(PySOR)] complexes, where PySOR=(2-methylsulphinyl)-pyridine and (2-n-propylsulphinyl)pyridine

Alkylsulphinylpyridine ligands containing three potential donor centres: N, S and O atoms and two complexes of general formula trans-[PtCl2(PEt3)PySOR)] (R = Me and Pr-n) were prepared and characterized by elemental analysis, i.r. spectroscopy, H-1- and P-31-n.m.r. and X-ray crystallography. The ambidentate ligands act in both situations as monodentate ligands, bonded to the metal exclusively through the nitrogen atom. The crystal structures revealed the occurrence of discrete molecules and, in both complexes, the Pt atoms are coordinated in square planar arrangements by two chloride ions, in a trans configuration, by the pyridine nitrogen atom, and by the phosphine P atom. The oxygen atoms do not take part in the complexation scheme.

Influence of annealing on X-ray diffraction of natural alexandrite

In this work we present results of X-ray diffraction using powder method, on natural alexandrite samples from Minas Gerais State (Brazil), as a function of a sequence of annealing. From these measurements we determine lattice parameters before (a = 9.405 Angstrom, b = 5.471 Angstrom, c = 4.409 Angstrom) and after annealing, and its structure is confirmed as orthorhombic. Measurements done after an annealing of 15 minutes at 700 degreesC and for 5 hours at 1000 degreesC indicate the migration of atoms present in the sample through different phases, which were also identified by Microprobe Analysis (WDS). However we have verified that such migration does not modify the structure. X-ray diffraction measurements have been carried out in conjunction with optical absorption in the UV-Vis as a function of annealing. (C) 2002 International Centre for Diffraction Data.

Doping of polyaniline and derivatives induced by X-ray radiation

Thin films of chemically synthesized polyaniline and poly(o-methoxyaniline) were exposed to ionizing X-ray radiation and characterized by radiation induced conductivity measurements, ultraviolet-visible spectroscopy, electron paramagnetic resonance, electrical conductivity and solubility measurements. Samples irradiated in vacuum or dry Oxygen atmosphere did not have their electronic spectra changed. However, under humid atmosphere the energy of the excitonic transition was decreased and accompanied by a great conductivity increase. The results indicate that doping of polyaniline can be induced by X-ray radiation which might be of great interest for applications on lithography and microelectronics.

Small-angle x-ray scattering study of the structural evolution of the drying of sonogels with the liquid phase exchanged by acetone

The structural evolution on the drying of wet sonogels of silica with the liquid phase exchanged by acetone, obtained from tetraethoxisilane sonohydrolysis, was studied in situ by small-angle x-ray scattering (SAXS). The periods associated to the structural evolution as determined by SAXS are in agreement with those classical ones established on basis of the features of the evaporation rate of the liquid phase in the obtaining of xerogels. The wet gel can be described as formed by primary particles (microclusters), with characteristic length a ∼ 0.67 nm and surface which is fractal, linking together to form mass fractal structures with mass fractal dimension D=2.24 in a length scale ξ∼6.7 nm. As the network collapses while the liquid/vapor meniscus is kept out of the gel volume, the mass fractal structure becomes more compacted by increasing D and decreasing ξ, with smoothing of the fractal surface of the microclusters. The time evolution of the density of the wet gels was evaluated exclusively from the SAXS parameters ξ, D, and a. The final dried acetone-exchanged gel presents Porod's inhomogeneity length of about 2.8 nm and apparently exhibits an interesting singularity D →3, as determined by the mass fractal modeling used to fit the SAXS intensity data for the obtaining of the parameters ξ and D.

CMS data processing workflows during an extended cosmic ray run

The CMS Collaboration conducted a month-long data taking exercise, the Cosmic Run At Four Tesla, during October-November 2008, with the goal of commissioning the experiment for extended operation. With all installed detector systems participating, CMS recorded 270 million cosmic ray events with the solenoid at a magnetic field strength of 3.8 T. This paper describes the data flow from the detector through the various online and offline computing systems, as well as the workflows used for recording the data, for aligning and calibrating the detector, and for analysis of the data. © 2010 IOP Publishing Ltd and SISSA.

Aligning the CMS muon chambers with the muon alignment system during an extended cosmic ray run

The alignment system for the muon spectrometer of the CMS detector comprises three independent subsystems of optical and analog position sensors. It aligns muon chambers with respect to each other and to the central silicon tracker. System commissioning at full magnetic field began in 2008 during an extended cosmic ray run. The system succeeded in tracking muon detector movements of up to 18 mm and rotations of several milliradians under magnetic forces. Depending on coordinate and subsystem, the system achieved chamber alignment precisions of 140-350 μm and 30-200 μrad, close to the precision requirements of the experiment. Systematic errors on absolute positions are estimated to be 340-590 μm based on comparisons with independent photogrammetry measurements. © 2010 IOP Publishing Ltd and SISSA.